Related papers: Detecting phylogenetic relations out from sparse c…

Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…

Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the same topology. In…

Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been investigated in the…

Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…

Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…

Tree-based ensemble methods such as random forests, gradient-boosted trees, and Bayesianadditive regression trees have been successfully used for regression problems in many applicationsand research studies. In this paper, we study ensemble…

Functional data analysis (FDA) and ensemble learning can be powerful tools for analyzing complex environmental time series. Recent literature has highlighted the key role of diversity in enhancing accuracy and reducing variance in ensemble…

Finding spanning trees under various constraints is a classic problem with applications in many fields. Recently, a novel notion of "dense" ("sparse") tree, and in particular spanning tree (DST and SST respectively), is introduced as the…

How do phylogenetic reconstruction algorithms go astray when they return incorrect trees? This simple question has not been answered in detail, even for maximum parsimony (MP), the simplest phylogenetic criterion. Understanding MP has…

In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…

We hereby present a solution to a semantic textual similarity (STS) problem in which it is necessary to match two sentences containing, as the only distinguishing factor, highly specific information (such as names, addresses, identification…

We investigated testing the likelihood of a phylogenetic tree by comparison to its subtree pruning and regrafting (SPR) neighbors, with or without re-optimizing branch lengths. This is inspired by aspects of Bayesian significance tests, and…

We introduce Tree-AMP, standing for Tree Approximate Message Passing, a python package for compositional inference in high-dimensional tree-structured models. The package provides a unifying framework to study several approximate message…

Recursive partitioning is the core of several statistical methods including CART, random forest, and boosted trees. Despite the popularity of tree based methods, to date, there did not exist methods for combining multiple trees into a…

The graph edit distance is used for comparing graphs in various domains. Due to its high computational complexity it is primarily approximated. Widely-used heuristics search for an optimal assignment of vertices based on the distance…

In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…

The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…

In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…

Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples…

The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…